fastaccess

Efficient random access to subsequences in FASTA files using byte-level seeking.

Installation

pip install fastaccess

From source (includes C++ backend for better performance):

pip install -e .

The C++ backend requires a C++17 compiler and CMake 3.15+. If unavailable, falls back to pure Python.

Quick Start

from fastaccess import FastaStore

fa = FastaStore("genome.fa")  # Builds index, caches for next time
seq = fa.fetch("chr1", 1000, 2000)  # 1-based inclusive coordinates

API

FastaStore(path, use_cache=True, cache_dir=None)

• path: Path to FASTA file (plain or gzip-compressed .fa.gz)
• use_cache: Save/load index from .fidx cache file
• cache_dir: Custom directory for cache file (useful for read-only FASTA directories)

Methods

Method	Description
fetch(name, start, stop, reverse_complement=False)	Fetch subsequence (1-based inclusive)
fetch_many(queries)	Batch fetch list of (name, start, stop) tuples
list_sequences()	Get all sequence names
get_length(name)	Get sequence length
get_description(name)	Get FASTA header description
get_info(name)	Get dict with name, description, length
rebuild_index()	Force rebuild index and update cache
is_cached()	Check if loaded from cache
cache_exists()	Check if cache file exists
get_cache_path()	Get cache file path
delete_cache()	Delete cache file

Errors

• KeyError: Sequence name not found
• ValueError: Invalid coordinates (start < 1, stop < start, stop > length)

Features

• Random access: Uses seek() to fetch only required bytes
• Index caching: 7-40x faster reloading via .fidx cache files
• Gzip support: Reads .fa.gz files directly
• 1-based inclusive coordinates: Standard bioinformatics convention
• Format support: Wrapped/unwrapped sequences, Unix/Windows line endings
• Uppercase output: All sequences returned uppercase

Performance

C++ Backend

Operation	Python	C++	Speedup
Index build (10MB)	70 ms	5 ms	13x
Reverse complement (8 KB)	0.21 ms	0.015 ms	14x
Small fetch (100 bp)	0.017 ms	0.017 ms	1x
Large fetch (100 KB)	0.36 ms	0.35 ms	1x

Check if C++ backend is active:

from fastaccess import using_cpp_backend
print(using_cpp_backend())  # True if available

Index Caching

Human genome (3 GB):
  First load:  ~2 seconds (builds index)
  With cache:  0.05 seconds (40x faster)

Cache is automatically invalidated when the FASTA file changes.

Example

from fastaccess import FastaStore

fa = FastaStore("hg38.fa")

# Get sequence info
print(fa.list_sequences())  # ["chr1", "chr2", ...]
print(fa.get_length("chr1"))  # 248956422

# Fetch regions
seq = fa.fetch("chr1", 1000, 2000)
rc = fa.fetch("chr1", 1000, 2000, reverse_complement=True)

# Batch fetch
regions = [("chr1", 1, 100), ("chr2", 500, 600)]
sequences = fa.fetch_many(regions)

Requirements

• Python 3.8+
• No runtime dependencies (pure Python fallback always works)

C++ backend (optional):

• C++17 compiler
• CMake 3.15+

Limitations

• ASCII sequences only (DNA/RNA)
• Gzip files require full decompression (no random access within compressed data)

License

MIT